David MountBioinformatics: Sequence and Genome Analysis 2nd Edition
Jin XiongEssential Bioinformatics
Jones & PevznerBioinformatics Algorithms
Baldi & BrunakBioinformatics: The Machine Learning Approach
Higgins & TaylorBioinformatics: Sequence, Structure & Databanks
NCBI Handbookhttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook
NCBI Handbookhttp://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook
EMBL-EBI Home Pagehttp://www.ebi.ac.uk/
Berg, Tymoczko & StryerBiochemistry, Fifth Edition
Genomics, Bioinformatics &Computational Biology
Computational Biology
Computational Molecular Biology
BioinformaticsGenomics
ProteomicsStructural Genomics
DatabasesMachine Learning
Robotics
Statistics & ProbabilityArtificial Intelligence
Graph Theory
Information Theory
Algorithms
Genomics, Bioinformatics &Computational Biology
Computational Biology
Computational Molecular Biology
BioinformaticsGenomics
ProteomicsStructural Genomics
What is Bioinformatics?
RNA Protein
DNA Phenotype
SelectionEvolution
Individuals
Populations
Biological Information
Computational Goals of Bioinformatics
• Learn & Generalize: Discover conserved patterns (models) of sequences, structures, interactions, metabolism & chemistries from well-studied examples.
• Prediction: Infer function or structure of newly sequenced genes, genomes, proteins or proteomes from these generalizations.
• Organize & Integrate: Develop a systematic and genomic approach to molecular interactions, metabolism, cell signaling, gene expression…
• Simulate: Model gene expression, gene regulation, protein folding, protein-protein interaction, protein-ligand binding, catalytic function, metabolism…
• Engineer: Construct novel organisms or novel functions or novel regulation of genes and proteins.
• Gene Therapy: Target specific genes, or mutations, RNAi to change a disease phenotype.
Central Paradigm of Molecular Biology
DNA RNA ProteinPhenotype
(Symptoms)
Molecular Biology of the Gene 1965
Challenges Understanding Genetic Information
GeneticInformation
MolecularStructure
BiochemicalFunction Phenotype
• Genetic information is redundant
• Structural information is redundant
• Genes and proteins are meta-stable
• Single genes have multiple functions
• Genes are one dimensional but function depends on three-dimensional structure
Redundancy in Genomic& Protein Sequences
• DNA is double-stranded• Genetic code• Acceptable amino-acid
replacements• Intron-exon variation
• Alternative splicing• Strain variations (SNPs)
• Sequencing errors